Difference between revisions of "Resources for Data Contributors"
(→5. Update Taxon Lists) |
Jim Balhoff (talk | contribs) |
||
| (32 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| + | The following instructions outline the resources used by Phenoscape curators for the annotation of evolutionary phenotypes. If you are a student intern, please refer to the [http://phenoscape.org/wiki/Student_Instructions Student Instructions] page for more information and links. | ||
| + | |||
| + | Data uploaded to the Phenoscape Knowledgebase are made available under a Creative Commons Attribution 3.0 Unported license (see [[Phenoscape data policy]]) | ||
| + | |||
==1. Download Most Recent Version of Phenex== | ==1. Download Most Recent Version of Phenex== | ||
| − | Phenex was developed by Phenoscape for annotation of evolutionary phenotypes. You can find instructions for downloading and installing Phenex at the [[Phenex|Phenex homepage]]. | + | Phenex was developed by Phenoscape for annotation of evolutionary phenotypes. You can find instructions for downloading and installing Phenex at the [[Phenex|'''Phenex homepage''']]. |
==2. Access Project Files== | ==2. Access Project Files== | ||
| − | Phenoscape project files are XML files (more specifically, they are in [http://nexml.org NeXML] format) created using Phenex and | + | Phenoscape project files are XML files (more specifically, they are in [http://nexml.org NeXML] format) created using Phenex and available on GitHub at https://github.com/phenoscape/phenoscape-data. |
| − | ==3. | + | ==3. Access PDFs for Curation == |
| − | |||
| − | + | Phenoscape maintains a collection of PDFs for curation. Please ask project personnel (Wasila or Paula) for access to the collection. | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
==4. Use Ontologies to Annotate Characters == | ==4. Use Ontologies to Annotate Characters == | ||
| Line 31: | Line 21: | ||
==5. Update Taxon Lists== | ==5. Update Taxon Lists== | ||
| − | Most project files require a taxonomic expert to review the taxonomy used in a publication and update to reflect current taxonomy. Please see instructions for [[Update Taxon Lists| '''updating taxon lists''']]. | + | Most project files require a taxonomic expert to review the taxonomy used in a publication and update to reflect current taxonomy. Please see instructions for [[Creating Taxon Lists| '''creating taxon lists''']] in Phenex or instructions for [[Update Taxon Lists| '''updating taxon lists''']] with valid taxon names. |
==6. Request New Terms for Ontologies== | ==6. Request New Terms for Ontologies== | ||
| − | Curation drives ontology development and many new terms and relationships need to be added. | + | Curation drives ontology development and many new terms and relationships need to be added. Submit requests for updates to the ontologies used in Phenoscape to the following term trackers: |
| + | |||
| + | * [https://github.com/cmungall/uberon/issues Uber Anatomy Ontology (Uberon) term tracker] | ||
| + | * [http://sourceforge.net/tracker/?group_id=76834&atid=595654 Phenotype and Trait Ontology (PATO) term tracker] | ||
| + | * [http://sourceforge.net/tracker/?group_id=224046&atid=2519810 Vertebrate Taxonomy Ontology (VTO) term tracker] | ||
| + | * [http://phenoscape.org/wiki/Ontologies#Fish_Collection_Codes_Vocabulary Collection Codes Vocabulary] | ||
| + | |||
| + | ==7. Edit the Anatomy Ontology == | ||
| + | * [http://phenoscape.org/wiki/Ontology_workflow Ontology Editing Guidelines] | ||
| − | == | + | ==8. Subscribe to Curator and Ontology Request Mailing Lists == |
| − | * | + | * Discussion of ontology development and Open Biomedical Ontologies community issues ''[https://groups.google.com/forum/#!forum/obo-discuss obo-discuss] |
| − | |||
| − | |||
[[Category:Curation]] | [[Category:Curation]] | ||
[[Category:Help]] | [[Category:Help]] | ||
Latest revision as of 01:17, 26 March 2019
The following instructions outline the resources used by Phenoscape curators for the annotation of evolutionary phenotypes. If you are a student intern, please refer to the Student Instructions page for more information and links.
Data uploaded to the Phenoscape Knowledgebase are made available under a Creative Commons Attribution 3.0 Unported license (see Phenoscape data policy)
Contents
1. Download Most Recent Version of Phenex
Phenex was developed by Phenoscape for annotation of evolutionary phenotypes. You can find instructions for downloading and installing Phenex at the Phenex homepage.
2. Access Project Files
Phenoscape project files are XML files (more specifically, they are in NeXML format) created using Phenex and available on GitHub at https://github.com/phenoscape/phenoscape-data.
3. Access PDFs for Curation
Phenoscape maintains a collection of PDFs for curation. Please ask project personnel (Wasila or Paula) for access to the collection.
4. Use Ontologies to Annotate Characters
The primary activity of a curator is to annotate the free-text characters from systematic studies using ontologies. Instructions for this activity can be found in the Phenoscape Guide to Character Annotation.
5. Update Taxon Lists
Most project files require a taxonomic expert to review the taxonomy used in a publication and update to reflect current taxonomy. Please see instructions for creating taxon lists in Phenex or instructions for updating taxon lists with valid taxon names.
6. Request New Terms for Ontologies
Curation drives ontology development and many new terms and relationships need to be added. Submit requests for updates to the ontologies used in Phenoscape to the following term trackers:
- Uber Anatomy Ontology (Uberon) term tracker
- Phenotype and Trait Ontology (PATO) term tracker
- Vertebrate Taxonomy Ontology (VTO) term tracker
- Collection Codes Vocabulary
7. Edit the Anatomy Ontology
8. Subscribe to Curator and Ontology Request Mailing Lists
- Discussion of ontology development and Open Biomedical Ontologies community issues obo-discuss
